Rice–wheat comparative genomics: Gains and gaps

Akila Wijerathna-Yapa Md. Harun-Or-Rashid BHOJA BASNET (2023, [Artículo])

CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA COMPARATIVE GENOMICS GENES GENETIC ENGINEERING BREEDING RICE WHEAT

Enhancement of plant variety protection and regulation using molecular marker technology

Yunbi Xu Jian Zhang Jiansheng LI (2022, [Artículo])

Plant Variety Protection Distinctness-Uniformity-Stability Essentially Derived Variety Molecular Markers Molecular Diagnostics Genetic Similarity CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA GENETICS GENETIC MARKERS PLANT BREEDING VARIETIES

Estudios de genética en poblaciones de abulón y sus aplicaciones en ordenamiento pesquero

RICARDO PEREZ ENRIQUEZ NOE DIAZ VILORIA JOSE LUIS GUTIERREZ GONZALEZ ALEJANDRA ARCINIEGA DE LOS SANTOS ADRIANA MAX AGUILAR Pedro Cruz Hernández Fernando Aranceta Garza (2016, [Artículo])

"Se presenta la integración de más de 10 años de investigación científica en genética de las poblaciones de abulón en México realizada en el CIBNOR. Esta investigación muestra cómo se pueden aplicar los marcadores genéticos tanto en estudios de genética poblacional como en identificación forense con la finalidad de contribuir al conocimiento aplicado para manejo de la pesquería. Se desarrollaron marcadores genéticos tipo microsatélites de ADN enfocados tanto al abulón azul Haliotis fulgens como amarillo Haliotis corrugata para diferenciación de poblaciones y análisis de parentesco. Un análisis de estructura genética de las poblaciones silvestres de ambas especies de abulón mostró homogeneidad genética en la costa del Pacífico en la región centro-sur de la Península de Baja California, México, pero con diferenciación genética en localidades distantes debido a un flujo genético limitado producto del aislamiento reproductivo. Por ello, no existen elementos que den soporte a un manejo pesquero delimitado por bancos en ambas especies. De manera particular, el abulón amarillo mostró una menor de diversidad genética que el azul, posiblemente debido a una mayor explotación pesquera histórica. Los resultados obtenidos en pruebas de parentesco han indicado que la retención larvaria en bancos específicos es reducida, por lo que ni la agregación de reproductores ni la liberación de larvas han mostrado ser estrategias eficientes para favorecer el incremento de reclutas en bancos definidos. Un análisis de perfiles genéticos con el gen de la lisina permitió la identificación de las especies de abulón que se capturan y enlatan en México. El análisis comparativo de perfi les genéticos, basado en el gen nuclear 18S de abulón y otros moluscos, detectó producto enlatado conteniendo especies de moluscos comercializadas falsamente como abulón, lo que puede constituirse como una herramienta forense en futuras disputas legales. Este tipo de aplicación es potencialmente utilizable con otros productos comestibles en los cuales se sospecha de prácticas fraudulentas, ya sea por captura o comercialización ilegal o por sustitución de contenidos en productos procesados."

"This is an integrative work of more than 10 years of research in population genetics of abalone in Mexico performed at CIBNOR. It shows how molecular tools have the potential to support abalone fisheries management through population genetics and forensic analyses. Microsatellite DNA markers were developed on blue (green for its name in English) Haliotis fulgens and yellow abalone (pink for its name in English) H. corrugata to be used for genetic differentiation on populations and for parentage analysis. The analysis of genetic structure on wild populations of both species revealed genetic homogeneity in the Pacific coast of the central region of the Baja California Peninsula, Mexico, with genetic differentiation on distant localities due to a limited gene flow as a result of reproduction isolation. From this result we suggest that no evidences were found supporting the management of the fishery based on individual abalone beds. Pink abalone shows lower genetic diversity than green abalone, possibly due to higher historical fishery exploitation. The parentage analysis suggested that larval retention within beds is reduced, indicating that neither broodstockaggregation nor the release of abalone larvae for stock enhancement are efficient strategies to increase recruitment in specific beds.

An analysis of the genetic profiles with the lysine gene allowed the identification of abalone species captured and processed in Mexico. The comparative analysis, based on the 18S gene, among abalone and other mollusks, detected canned product containing mollusks that are commercialized allegedly as abalone or ‘abalone type’, which could constitute a forensic tool in future legal disputes. This type of application can also be used with other edible products in which fraudulent practices are suspected either because of illegal catch or commercialization or substitution in processed products."

Análisis forense, diversidad genética, gen 18S, genética de poblaciones, marcadores genéticos, retención larvaria Forensic analysis, genetic diversity, 18S gene, genetic markers, population genetics, larval retention BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA GENÉTICA GENÉTICA DE POBLACIONES GENÉTICA DE POBLACIONES

Autotrophic denitrification of nitrate rich wastewater in fluidized bed reactors using pyrite and elemental sulfur as electron donors

Maria Federica Carboni Simon Mills SONIA LORENA ARRIAGA GARCIA Gavin Collins Umer Zeeshan Ijaz Piet Nicolaas Luc Lens (2022, [Artículo])

"This study compared denitrification performances and microbial communities in fluidized bed reactors (FBRs) carrying out autotrophic denitrification using elemental sulfur (S0) and pyrite (FeS2) as electron donors. The reactors were operated for 220 days with nitrate loading rates varying between 23 and 200 mg N-NO-3 /Lmiddotd and HRT between 48 and 4 h. The highest denitrification rates achieved were 142.2 and 184.4 mg NNO-3 /Lmiddotd in pyrite and sulfur FBRs, respectively. Pyrite-driven denitrification produced less SO2- 4 and no buffer addition was needed to regulate the pH. The sulfur FBR needed instead CaCO3 to maintain the pH neutral and consequentially more sludge was produced (CaSO4 precipitation). The active community of pyrite-based systems was investigated and Azospira sp., Ferruginibacter sp., Rhodococcus sp. and Pseudomonas sp. were the predominant genera, while Thiobacillus sp. and Sulfurovum sp. dominated the active community in the sulfur FBR. However, Thiobacillus sp. became more dominant when operating at elevated nitrogen loading rate. Patterns of diversity and microbial community assembly were assessed and revealed three distinct stages of microbial community succession which corresponded with the operation of a period of high influent nitrate concentration (135 mg N-NO-3 /L). It is proposed that a high degree of functional redundancy in the initial microbial communities may have helped both reactors to respond better to such high influent nitrate concentration."

Pyrite Elemental sulfur Fluidized bed rector Nitrogen removal 16S rRNA Community assembly CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA

Genetic structure analysis and identifying key founder inbred lines in diverse elite sub-tropical maize inbred lines

Melaku Gedil Ana Luisa Garcia-Oliveira Nnanna Unachukwu Cesar Petroli Sarah Hearne Abebe Menkir (2023, [Artículo])

Genetic Relationship Desirable Target Traits Parental Selection CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA GENETIC STRUCTURES INBRED LINES MAIZE BREEDING PROGRAMMES

Efficacy of plant breeding using genomic information

Osval Antonio Montesinos-Lopez Alison Bentley Carolina Saint Pierre Leonardo Abdiel Crespo Herrera Morten Lillemo Jose Crossa (2023, [Artículo])

Genomic Selection Genomic Prediction Genomic Best Linear Unbiased Predictor CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA PLANT BREEDING GENOMICS MARKER-ASSISTED SELECTION ENVIRONMENT

Surviving “Los Sures”: An anthropological reflection on the Nuyoricans lived experiences in South Williamsburg, Brooklyn and the current urban context of gentrification in New York City

Victor Vazquez Ashley McAfee (2021, [Artículo, Artículo])

The following article presents an anthropological and historical reflection on the Puerto Rican inner-city neighborhood better known as “Los Sures” in South Williamsburg, Brooklyn, New York City (nyc). The analysis will explore the contemporary academic discussion regarding the following concepts: poverty, the welfare State, the discourse surrounding welfare recipient’s culture, inner-city living conditions, and the current context of gentrification. Methodologically, the article presents an ethnographic reflection based on fieldwork experiences and interviews conducted on residents of the previous “Los Sures” and still living in nyc. Finally, we present a critical reflection on the poverty, welfare State policy, and shed light on the difficulties faced by Puerto Rican migrants and their struggle to preserve the Puerto Rican legacy in the now nyc and gentrified “Los Sures”.

Nuyoricans gentrification; urban studies gentrification HUMANIDADES Y CIENCIAS DE LA CONDUCTA HUMANIDADES Y CIENCIAS DE LA CONDUCTA

Editorial: Model organisms in plant science: Maize

Manje Gowda (2023, [Artículo])

Model Organism Genomic Selection CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA MAIZE PLANT SCIENCES RESEARCH CROP IMPROVEMENT PLANT PHYSIOLOGY PLANT BREEDING

De Novo assembly and annotation of the Pacific calico scallop (Argopecten ventricosus) transcriptome for immune-related gene discovery

RUTH ESCAMILLA MONTES GENARO DIARTE PLATA GABRIELA BERENICE MENDOZA MALDONADO Aarón Barraza Celis Carlos Eliud Angulo Valadez Seyed Hossein Hoseinifar Jesús Arturo Fierro Coronado ANTONIO LUNA GONZALEZ (2022, [Artículo])

"Invertebrates' immune defense mechanisms play a critical role in pathogen recognition and elimination. De novo assembly and annotation of the Argopecten ventricosus transcriptome were performed for the immune-related gene identification. Scallops (height: 4.4 cm) were challenged with inactivated Vibrio parahaemolyticus IPNGS16. The RNA from different tissues was pooled for a single cDNA library construction sequenced by NextSeq 500 platform 2×75 paired‐end chemistry. Before de novo assembling with Trinity, reads were analyzed with FastQC, Trimmomatic, and Prinseq. Assembled sequences were analyzed by CD-HIT-EST and TransDecoder. The corresponding annotation was performed against NCBI-nr, RefSeq protein, and KAAS (KEGG) databases. The Trinity assembly yielded 107,516 contigs. TransDecoder yielded 25,285 sequences as CDSs of which, 16,123 were annotated against the NCBI-nr protein, most of them scored with Crassostrea gigas data. Gene ontology mapped sequences (15,262) were classified in molecular functions (~13,000), cellular components (~11,000), and biological processes (~13,000). The KAAS analysis showed biological categories for metabolism (13%), cellular processes (12%), genetic information processing (10%), organismal systems (19%), environmental information (13%), and human diseases (33 %). Within the organismal systems, 467 immune-related genes (KO) were identified. Sixty-four immune-related genes were annotated/blasted against the NCBI-nr and RefSeq protein databases. An RT-qPCR was performed to analyze the expression level of immune-related genes obtained in the transcriptome analysis in scallops (height 4.5 cm) treated with probiotic bacilli added to culture water. Bacilli significantly increased the expression of the HSP70 and PGRP genes. The gene transcripts analysis of A. ventricosus will better understand its immune response against pathogens in culture systems."

Argopecten ventricosus, calico scallop, transcriptome, bivalve, immune genes BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOLOGÍA ANIMAL (ZOOLOGÍA) INMUNOLOGÍA INMUNOLOGÍA

Silage maize as a potent candidate for sustainable animal husbandry development—perspectives and strategies for genetic enhancement

Yogesh Vikal Manje Gowda (2023, [Artículo])

Brown Mid-Rib Genomic Selection CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA BIOMASS SILAGE DIGESTIBILITY GENOME-WIDE ASSOCIATION STUDIES MARKER-ASSISTED SELECTION MAIZE